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Old 09-27-2014, 03:19 PM   #1
Palgrave
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Default Get loop sequence from miRBase

Does anyone know a way to extract the loop sequence from the miRNA hairpin. Basically I need to extract the part that is between the 3p- and 5p part of the hairpin.
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Old 09-28-2014, 01:06 AM   #2
dpryan
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Just align the 5p and 3p sequences to the hairpin sequence and take the bit between them.
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Old 09-28-2014, 01:13 AM   #3
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Quote:
Originally Posted by dpryan View Post
Just align the 5p and 3p sequences to the hairpin sequence and take the bit between them.
I have tried, but struggle to find a command that works.
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Old 09-28-2014, 01:33 AM   #4
dpryan
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I would expect that either biopython or bioperl should make this relatively straight forward. The idea is to either use base python string matching or the pairwise2 module and global alignment.
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